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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendMetaboLights.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendMetaboLights_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MsBackendMetaboLights.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MsBackendMetaboLights/DESCRIPTION’ ... OK
* this is package ‘MsBackendMetaboLights’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MsBackendMetaboLights’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MsBackendMetaboLights.Rd: MsBackendMzR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MsBackendMetaboLights-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MsBackendMetaboLights
> ### Title: MsBackend representing MS data from MetaboLights
> ### Aliases: MsBackendMetaboLights MsBackendMetaboLights-class
> ###   backendInitialize,MsBackendMetaboLights-method
> ###   backendMerge,MsBackendMetaboLights-method
> ###   backendRequiredSpectraVariables,MsBackendMetaboLights-method
> ###   mtbls_sync
> 
> ### ** Examples
> 
> 
> library(MsBackendMetaboLights)
> 
> ## List files of a MetaboLights data set
> mtbls_list_files("MTBLS39")
[1] "FILES"                                                                                                          
[2] "a_MTBLS39_the_plasticity_of_the_grapevine_berry_transcriptome_metabolite_profiling_mass_spectrometry.txt"       
[3] "i_Investigation.txt"                                                                                            
[4] "m_MTBLS39_the_plasticity_of_the_grapevine_berry_transcriptome_metabolite_profiling_mass_spectrometry_v2_maf.tsv"
[5] "metexplore_mapping.json"                                                                                        
[6] "s_MTBLS39.txt"                                                                                                  
> 
> ## Initialize a MsBackendMetaboLights representing all MS data files of
> ## the data set with the ID "MTBLS39". This will download and cache all
> ## files and subsequently load and represent them in R.
> 
> be <- backendInitialize(MsBackendMetaboLights(), "MTBLS39")
Used data files from the assay's column "Raw Spectral Data File" since none were available in column "Derived Spectral Data File".
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN063B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN063C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS063B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS063C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083C.cdf'
Error: database disk image is malformed
Error: database disk image is malformed
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
MetaboLights-utils 0.348   0.03   6.852
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   14.                 ├─DBI::dbExecute(conn, paste0("RELEASE SAVEPOINT ", name_quoted))
   15.                 └─DBI::dbExecute(conn, paste0("RELEASE SAVEPOINT ", name_quoted))
   16.                   ├─DBI::dbSendStatement(conn, statement, ...)
   17.                   └─DBI::dbSendStatement(conn, statement, ...)
   18.                     ├─DBI::dbSendQuery(conn, statement, ...)
   19.                     └─RSQLite::dbSendQuery(conn, statement, ...)
   20.                       └─RSQLite (local) .local(conn, statement, ...)
   21.                         ├─methods::new(...)
   22.                         │ ├─methods::initialize(value, ...)
   23.                         │ └─methods::initialize(value, ...)
   24.                         └─RSQLite:::result_create(conn@ptr, statement)
  
  [ FAIL 6 | WARN 3 | SKIP 0 | PASS 39 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/MsBackendMetaboLights.Rcheck/00check.log’
for details.